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Gene identifier synonym table standard and/or repository?

Suzanna Lewis suzi at fruitfly.org
Thu Feb 13 10:19:24 PST 2003


Hi,

I'm double-checking here that we are getting this loaded
into the DB as well. They don't currently appear in amigo,
nor can they be searched, but Brad and I are talking about
how to do that.

-S

On Thursday, February 13, 2003, at 09:33 AM, Valerie Wood wrote:

>
>
> i utilize this column for S. pombe too. btw I use "|" to separate  
> multiple
> synonyms, is this correct?
>
>
>
> On Thu, 13 Feb 2003, Tanya Berardini wrote:
>
>>
>> In the TAIR gene_association file, column 11 is populated with
>> synonyms/aliases for the annotated object.  These may include  
>> BAC-based
>> names from the genome sequencing phase, full names for the lettered
>> abbreviations (e.g. EMF1 is embryonic flower 1), other aliases for  
>> that
>> gene (e.g. ATROP4 = ROP4 = ATGP3 = ARAC5), Arabidopsis Genome  
>> Initiative
>> (AGI) locus names (of the format ATxgXXXXX), and gene product names.
>>
>> Tanya
>>
>>
>> On Thu, 13 Feb 2003, Suzanna Lewis wrote:
>>
>>> In the gene associations table the 11th column is listed
>>> as DB_object_synonym. I believe that this column was
>>> added especially to address this issue. It allows for
>>> white space and has a cardinality of 0, 1, or >1. I think
>>> this is a more a problem of the organism databases not
>>> having made the switch to providing this information
>>> when the gene associations are submitted. Column 12
>>> is the db object type (is it a gene, or a protein, or a .....)
>>> and column 13 is the taxon. I think if these were being
>>> populated it would perhaps help you.
>>>
>>> Any chance of this being put into practice annotators??
>>>
>>> -S
>>>
>>> On Thursday, February 13, 2003, at 07:54 AM, Fritz Roth wrote:
>>>
>>>> Greetings GOphiles,
>>>>
>>>> We are working on some new software that uses GO annotation, and we
>>>> would really like it to support all GO-annotated organisms.  Our  
>>>> chief
>>>> barrier to doing this is the lack of gene identifier synonym tables
>>>> for each organism (so that users can enter gene names rather than
>>>> being restricted to MOD IDS, e.g., SGD or MGI IDs).
>>>>
>>>> Is there an agreed GO Consortium standard for gene identifier  
>>>> synonym
>>>> tables (could be as simple as tab-delimited text with a
>>>> synonym-uniqueID pair on each line).  If so, is there a repository  
>>>> for
>>>> such files?  Or is this a GMOD question?
>>>>
>>>> Thanks!
>>>> Fritz Roth
>>>>
>>>> -------------------------------------------------
>>>> Frederick P. Roth, Asst. Professor
>>>> Harvard Medical School
>>>> Dept. of Biological Chemistry and Molecular Pharmacology
>>>> 250 Longwood Avenue, SGMB-322, Boston, MA 02115
>>>> (617) 432-3551 phone            (617) 432-3557 FAX
>>>> froth at hms.harvard.edu           http://llama.med.harvard.edu
>>>> -------------------------------------------------
>>>>
>>>>
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>>>
>>>
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>>
>> ---------------------------------------------------------------------- 
>> ---------
>> Tanya Berardini, Ph.D.			tberardi at acoma.stanford.edu
>> The Arabidopsis Information Resource	FAX: (650) 325-6857
>> Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 325
>> Department of Plant Biology		URL: http://arabidopsis.org/
>> 260 Panama St.
>> Stanford, CA 94305
>> ---------------------------------------------------------------------- 
>> ---------
>>
>>
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>
> ----------------------------------------------------------------------- 
> -----------
> Valerie Wood		       Tel: 01223 494954
> S. Pombe Genome Project	       Fax: 01223 494919
> The Sanger Institute           email: val at sanger.ac.uk
> Wellcome Trust Genome Campus   http://www.sanger.ac.uk/Projects/S_pombe
> Cambridge
> CB10 1SA
>
>


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